LPCAT1

lysophosphatidylcholine acyltransferase 1, the group of MicroRNA protein coding host genes|EF-hand domain containing|1-acylglycerol-3-phosphate O-acyltransferases

Basic information

Region (hg38): 5:1456480-1524282

Previous symbols: [ "AYTL2" ]

Links

ENSG00000153395

∙ NCBI:79888 ∙ OMIM:610472 ∙ HGNC:25718 ∙ Uniprot:Q8NF37 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LPCAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPCAT1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1 clinvar	1
missense			28 clinvar	1 clinvar		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	1	1

Variants in LPCAT1

This is a list of pathogenic ClinVar variants found in the LPCAT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
5-1463683-C-T	not specified	Uncertain significance (Dec 04, 2023)	3119729
5-1463733-G-A	not specified	Likely benign (Aug 26, 2024)	3539148
5-1463742-G-A	not specified	Uncertain significance (Apr 24, 2024)	3291161
5-1463773-G-T	not specified	Uncertain significance (Jan 10, 2023)	2475317
5-1463797-C-T	not specified	Uncertain significance (Nov 09, 2024)	3539151
5-1463812-T-C	not specified	Uncertain significance (May 14, 2024)	3291159
5-1463817-G-C		Likely benign (Apr 01, 2022)	2655277
5-1466761-T-G	not specified	Uncertain significance (Aug 19, 2024)	3539143
5-1466868-C-T	not specified	Uncertain significance (Oct 05, 2021)	2393279
5-1470826-C-T		Benign (May 18, 2018)	716860
5-1470827-T-C	not specified	Uncertain significance (Dec 20, 2021)	3119728
5-1470865-C-T		Benign (May 18, 2018)	723828
5-1470866-C-T	not specified	Uncertain significance (Aug 19, 2023)	2595324
5-1470869-C-A		Uncertain significance (May 03, 2020)	156208
5-1470875-A-G	not specified	Uncertain significance (May 17, 2023)	2547124
5-1470924-T-C	not specified	Uncertain significance (Sep 13, 2023)	2623603
5-1474027-G-A	not specified	Uncertain significance (Sep 20, 2024)	3539141
5-1474036-A-G	not specified	Uncertain significance (May 25, 2022)	2207915
5-1474070-A-C	not specified	Likely benign (Nov 20, 2024)	3539142
5-1474561-C-T	not specified	Uncertain significance (Sep 30, 2024)	3539152
5-1474569-C-T	not specified	Uncertain significance (Jun 29, 2022)	2299182
5-1474576-G-A	not specified	Uncertain significance (Apr 17, 2023)	2537102
5-1474576-G-C	not specified	Uncertain significance (May 17, 2023)	2547122
5-1474603-C-G	not specified	Uncertain significance (Aug 28, 2024)	3539144
5-1474606-C-T	not specified	Uncertain significance (Oct 14, 2023)	3119733

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPCAT1	protein_coding	protein_coding	ENST00000283415	14	67498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.137	0.863	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	254	337	0.753	0.0000233	3417
Missense in Polyphen		74	131.76	0.56162		1261
Synonymous	-1.07	167	150	1.11	0.0000118	1118
Loss of Function	3.62	7	27.5	0.255	0.00000154	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000890	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Possesses both acyltransferase and acetyltransferase activities (PubMed:16864775, PubMed:21498505). Activity is calcium-independent (By similarity). Mediates the conversion of 1- acyl-sn-glycero-3-phosphocholine (LPC) into phosphatidylcholine (PC) (PubMed:21498505). Displays a clear preference for saturated fatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donors and acceptors, respectively (PubMed:16704971). May synthesize phosphatidylcholine in pulmonary surfactant, thereby playing a pivotal role in respiratory physiology (PubMed:16864775). Involved in the regulation of lipid droplet number and size (PubMed:25491198). {ECO:0000250|UniProtKB:Q3TFD2, ECO:0000269|PubMed:16864775, ECO:0000269|PubMed:21498505, ECO:0000269|PubMed:25491198}.;
Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Neutrophil degranulation;Acyl chain remodelling of PG;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Acyl chain remodelling of PC;Synthesis of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

pRec: 0.166

Intolerance Scores

loftool: 0.146
rvis_EVS: -0.84
rvis_percentile_EVS: 11.4

Haploinsufficiency Scores

pHI: 0.0941
hipred: Y
hipred_score: 0.685
ghis: 0.554

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.638

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Lpcat1
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: phosphatidic acid biosynthetic process;phosphatidylcholine biosynthetic process;phospholipid biosynthetic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;surfactant homeostasis;neutrophil degranulation;positive regulation of protein catabolic process;retina development in camera-type eye;negative regulation of phosphatidylcholine biosynthetic process
Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;lipid droplet;plasma membrane;membrane;integral component of membrane;azurophil granule membrane
Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;calcium ion binding;2-acylglycerol-3-phosphate O-acyltransferase activity;1-alkenylglycerophosphocholine O-acyltransferase activity;1-acylglycerophosphocholine O-acyltransferase activity;1-alkylglycerophosphocholine O-acyltransferase activity;1-alkylglycerophosphocholine O-acetyltransferase activity